Background <p>The litter size of goats is a key factor affecting their reproductive performance. The ovary plays a central role in the reproductive process of goats. However, the relationship between the dynamic changes in the ovarian proteome and the prolific traits of goats remains unclear. The Jining Grey Goat, an excellent dual-purpose meat and skin breed in China, is famous for its distinctive coat color characteristics and high reproductive performance.</p> Methods <p>It is an ideal animal model for studying goat reproductive performance. We selected 8 Jining Grey Goats and divided them into a single-birth group (<i>n</i> = 4) and a multiple-birth group (<i>n</i> = 4) to collect ovarian tissue samples. The iTRAQ technology, bioinformatics analysis, and Western blot were employed to investigate protein expression differences in ovarian tissues of goats with varying litter sizes.</p> Results <p>A total of 468 differentially expressed proteins (DEPs) were identified, of which 255 were up-regulated and 213 were down-regulated. GO enrichment analysis showed that these DEPs were mainly involved in biological processes such as cellular processes and metabolic processes, as well as molecular functions such as actin filament binding and calcium ion binding. KEGG pathway enrichment analysis revealed that the focal adhesion, Oxytocin Signaling Pathway, and PPAR Signaling Pathway were significantly enriched. Protein interaction network analysis identified <i>CAV1</i>, <i>FLNA</i>, <i>CNN1</i>, <i>TAGLN</i>, and <i>MYH11</i> as key candidate proteins, and Western blot verification results were consistent with the iTRAQ trends.</p> Conclusion <p>This study revealed the molecular regulatory network of prolific traits in Jining Grey Goats from a proteomics perspective, providing a new insight into analyzing the genetic basis of goat fertility and serving as a reference for studying reproductive traits in other economically significant animals.</p>